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. 2021 Jan 6:10:4.
doi: 10.12688/f1000research.28022.2. eCollection 2021.

BioPAN: a web-based tool to explore mammalian lipidome metabolic pathways on LIPID MAPS

Caroline Gaud  1 , Bebiana C Sousa  2 , An Nguyen  1 , Maria Fedorova  3 , Zhixu Ni  3 , Valerie B O'Donnell  4 , Michael J O Wakelam  2 , Simon Andrews  1 , Andrea F Lopez-Clavijo  2
Affiliations

BioPAN: a web-based tool to explore mammalian lipidome metabolic pathways on LIPID MAPS

Caroline Gaud et al. F1000Res. .

Abstract

Lipidomics increasingly describes the quantification using mass spectrometry of all lipids present in a biological sample. As the power of lipidomics protocols increase, thousands of lipid molecular species from multiple categories can now be profiled in a single experiment. Observed changes due to biological differences often encompass large numbers of structurally-related lipids, with these being regulated by enzymes from well-known metabolic pathways. As lipidomics datasets increase in complexity, the interpretation of their results becomes more challenging. BioPAN addresses this by enabling the researcher to visualise quantitative lipidomics data in the context of known biosynthetic pathways. BioPAN provides a list of genes, which could be involved in the activation or suppression of enzymes catalysing lipid metabolism in mammalian tissues.

Keywords: Biosynthetic pathway analysis; LIPID MAPS; Lipidomics; lipid profiling.; lipids.

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Conflict of interest statement

No competing interests were disclosed.

Figures

Figure 1.
Figure 1.. Main results page view for BioPAN.
Pathways are displayed as an interactive graph at the centre of the screen. Users have control over the information presented in the graph using the menus on the left side panel and results tables are displayed at the bottom of the screen.
Figure 2.
Figure 2.. BioPAN lipid networks.
Lipid network graphs exported from BioPAN for the liver ( A) and the cerebral cortex ( B) of aged mice compared to young mice . Green nodes correspond to active lipids and green shaded arrows to active pathways. Reactions with a positive Z score have green arrows while negative Z scores are coloured purple. Pathways options: aged condition of interest, young control condition, lipid type, active status, subclass level, reaction subset of lipid data, p value 0.05, and no paired-data.
Figure 3.
Figure 3.. BioPAN fatty acids networks.
FA graphs exported from BioPAN tool for the liver ( A) and the cerebral cortex ( B) of aged mice compared to young mice . Green nodes correspond to active lipids and green shaded arrows to active pathways. Reactions with a positive Z score have green arrows while negative Z scores are coloured purple. Pathways options: aged condition of interest, young control condition, lipid type, active status, subclass level, reaction subset of lipid data, p value 0.05, and no paired-data.
See this image and copyright information in PMC

References

    1. Slatter DA, Aldrovandi M, O’Connor A, et al. : Mapping the Human Platelet Lipidome Reveals Cytosolic Phospholipase A 2 as a Regulator of Mitochondrial Bioenergetics during Activation. Cell Metab. 2016;23(5):930–944. 10.1016/j.cmet.2016.04.001 - DOI - PMC - PubMed
    1. Quehenberger O, Armando AM, Brown AH, et al. : Lipidomics reveals a remarkable diversity of lipids in human plasma. J Lipid Res. 2010;51(11):3299–3305. 10.1194/jlr.M009449 - DOI - PMC - PubMed
    1. Hartler J, Trötzmüller M, Chitraju C, et al. : Lipid data analyzer: Unattended identification and quantitation of lipids in LC-MS data. Bioinformatics. 2011;27(4):572–577. 10.1093/bioinformatics/btq699 - DOI - PubMed
    1. Ni Z, Angelidou G, Lange M, et al. : LipidHunter Identifies Phospholipids by High-Throughput Processing of LC-MS and Shotgun Lipidomics Datasets. Anal Chem. 2017;89(17):8800–8807. 10.1021/acs.analchem.7b01126 - DOI - PubMed
    1. Tsugawa H, Cajka T, Kind T, et al. : MS-DIAL: Data Independent MS/MS Deconvolution for Comprehensive Metabolome Analysis. Nat Methods. HHS Public Access.2015;12(6):523–526. 10.1038/nmeth.3393 - DOI - PMC - PubMed

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